The present invention pertains to a method for isolating a target nucleic acid including small target nucleic acids from a sample, said method comprising at least the following steps a) binding at least a portion of the target nucleic acid including small target nucleic acids to a nucleic acid binding solid phase comprised in a column by passing the sample through said column, b) performing an enzymatic and/or chemical treatment on the nucleic acid binding solid phase while the target nucleic acid is bound to said solid phase, c) collecting at least a portion of the small target nucleic acids released from the solid phase during said treatment of step b) as flow-through, d) contacting said flow-through which comprises small target nucleic acids mixed with a recovery solution with a nucleic acid binding solid phase for binding the contained small target nucleic acids to said nucleic acid binding solid phase, e) optionally performing an elution. The present invention results in a considerable increase in the yield of small target nucleic acids in the isolated target nucleic acid because it allows to efficiently capture and recover small target nucleic acids.